Peptides and Protein Chemistry 2; Protein Structure, Folding, Insulin. Flashcards
What different functional ways can proteins be described by?
- Enzymes; accelerate biochemical reactions
- Structural; form biological structures
- Storage; of AAs
- Transport; carry important substances
- Hormonal; coordination of organism’s activity
- Receptors; signal transduction
- Motor proteins; movement
- Defense; immune system
What are the different ways you can classify a protein by its structure/shape?
- Globular ‘spherical’; many different folds (tertiary structuers)
- Fibrous; extended shape, generally structural proteins
How can proteins be classified in terms of cell localisation?
- Membrane; in direct physical contact with a membrane, generally water insoluble
- Soluble; water soluble, can be anywhere in the cell e.g. nucleus, cytosol.
What is the structure of a protein determined by?
Its amino acid sequence; primary structure
What is the function of a protein determined by?
Its shape; tertiary and sometimes quaternary structure
What is meant by a ‘sequence motif’?
Clusters of conserved residues within the sequence; carrying out a particular function/form a particular structure that is important for the protein, conserved between different species.
What is meant by absolute/similar/non-conservation of a protein’s surface? Where does insulin fit-in?
- Absolute; residue is always the same e.g. Asp
- Similar; residue is generally similar e.g. negatively charged
- Non-conservation; different residue in different species
Insulin is highly conserved; porcine and human insulin only differ in a single AA and bovine by 3 AAs.
What techniques can be used to determine protein structure?
- X-ray crystallography
- NMR spectroscopy
What covalent protein structure stabilising forces exist?
- Peptide bonds
- Disulfide bridges
What noncovalent protein structure stabilising forces exist?
- Hydrogen bonds
- Van der Waals
- Hydrophobic interactions
- π-π overlap (e- delocalisation)
- Electrostatic interactions (ionic and salt bridges)
Where are peptide bonds present and how can they be broken?
- Between AAs
- Broken down to individual AAs by:
> hydrolysis in harsh chemical conditions with 6M acid/alkali,
> proteases/proteolytic enzymes under physiological conditions
Where are disulfide bonds present and how can they be broken?
- Between two Cys residues via thiol (R-SH) groups
- Broken down by reduction with β-mercaptoethanol reforming cysteines
How strong is a H-bond/what influences the strength, and how are they disrupted?
- Depend on angle; optimum orientation requires X-H to point directly to lone pair (2 - 25 kJ mol-1)
- Disrupted by heat
- N, O, F = H-bond acceptors (lone pairs) and donors if H attached
How strong are van der Waals interactions, where do they occur and how can they be disrupted?
- 0.5 - 4 kJ mol-1
- Interactions between close atoms (short range dipole-dipole)
- Easily disrupted by heat or denaturing agents
Where does π-π overlap occur and how is it disrupted?
- Between π electron clouds delocalised over rings + bonds
- Disrupted by heat
How strong are electrostatic bonds/ionic interactions/salt bridges and how are they broken?
- 25 - 50 kJ mol-1
- Inversely proportional to the distance between two charged groups
- Broken by changes in pH or high ionic strength
How do hydrophobic interactions come to be?
They are non-polar side chains of AAs forced together in aqueous environments in order to minimise their disruptive effect on the H-bonding network of water molecules.
Where on a protein do charged/polar residues normally map to in soluble proteins?
The surface of soluble proteins, inc. hydrophilic residues.
Where in a protein do non-polar residues normally map to in a soluble protein?
To the hydrophobic core; non-polar/hydrophobic AAs grouped here away from direct contact with H2O.
Can soluble proteins have hydrophobic surface regions?
Yes; hydrophobic regions are not only present in the centre. Exposed surface hydrophobic side chains form surfaces for protein-protein interactions, with exposed residues forming ligand binding clefts such as active sites in enzymes.
How do proteins undergo folding to a stable low energy conformation?
- Folding begins w/formation of local segments of secondary structure
- A ‘molten globule’ can form by ‘hydrophobic collapse’; all hydrophobic side chains suddenly clumping together
- This is where the secondary structure elements of the protein are mostly formed
- Burial of hydrophobic side chains, exposure of polar/charged side chains to form H-bonds w/water, H-bonding and salt-bridging interactions.
What are chaperone proteins?
They assist in the proper folding of proteins in the cell via directed pathways etc
How are proteins denatured?
Extreme changes of pH, temperature or chemical agents such as detergents.
What is the result of amyloid/fibril formation?
These are non-native/abnormal structures that can cause the build-up of aggregates e.g. amyloid in Alzheimer’s Disease (changes in secondary structure?)
